Microspatial population genetic structure of the Mediterranean shrub Fumana thymifolia

Fumana thymifolia (Cistaceae) is an insect-pollinated, gravity-dispersed evergreen shrub, which is a common component of fire-prone Mediterranean shrubland ecosystems. Despite the availability of basic knowledge on its ecology, little is known of its breeding system and no information is available on its population genetic structure. We explored the within-population genetic structure of this species using amplified fragment length polymorphism (AFLP) molecular markers and related this to predictions based on its breeding system, pollen and seed dispersal. Existing information on the reproductive ecology of F. thymifolia was supplemented by artificial pollination experiments. We determined that self-fertilisation can occur in F. thymifolia but results in reduced fruit set. Significant genetic structuring was detected within the population, a likely consequence of localised seed dispersal in combination with a mixed mating system. In a study site covering approximately 0.5 ha, amova revealed that approximately 9% of genetic variability was distributed among population subsamples. Significant spatial genetic structure was detected, with kinship coefficients being significantly elevated above the null expectation in the first six distance classes (maximum 5 m), and a value of Sp of up to 0.0342, comparable with species having similar ecological characteristics. Weak isolation by distance at the plot scale was detected, suggesting that insect-mediated pollen flow is non-random, despite being more extensive than seed dispersal. Fumana thymifolia provides a promising model for the investigation of both short- and long-term population dynamics in relation to fire frequency within this plant community.     

A new cost‐distance model for human accessibility and an evaluation of accessibility bias in permanent vegetation plots in Great Smoky Mountains National Park,USA

Question: Can a new cost‐distance model help us to evaluate the potential for accessibility bias in ecological observations? How much accessibility bias is present in the vegetation monitoring plots accumulated over the last three decades in Great Smoky Mountains National Park? Location: Great Smoky Mountains National Park, North Carolina and Tennessee, USA. Methods: Distance, slope, stream crossings, and vegetation density were incorporated into a least‐cost model of energetic expenditure for human access to locations. Results: Estimated round‐trip energy costs for the park ranged from 0 to 1.62 × 10⁵ J kg^?1. The estimated round‐trip energetic expenditure for the surveys ranged from 53 to 1.51 × 10⁵ J kg^?1. Their distribution was more accessible than the random expectation. Ten (17%) of the vegetation types in the park are significantly under‐sampled relative to their area, and 16 (29%) are over‐sampled. Plots in 18 of the 40 vegetation types exhibited a significant positive correlation with accessibility. Conclusions: The least‐cost model is an improvement over previous attempts to quantify accessibility. The bias in plot locations suggests using a least‐cost model to test for bias in cases in which human accessibility is confounded with other sources of ecosystem variation.     

Regional analysis of the impacts of climate change on cheatgrass invasion shows potential risk and opportunity

Interactions between climate change and non-native invasive species may combine to increase invasion risk to native ecosystems. Changing climate creates risk as new terrain becomes climatically suitable for invasion. However, climate change may also create opportunities for ecosystem restoration on invaded lands that become climatically unsuitable for invasive species. Here, I develop a bioclimatic envelope model for cheatgrass ( Bromus tectorum ), a non-native invasive grass in the western US, based on its invaded distribution. The bioclimatic envelope model is based on the Mahalanobis distance using the climate variables that best constrain the species' distribution. Of the precipitation and temperature variables measured, the best predictors of cheatgrass are summer, annual, and spring precipitation, followed by winter temperature. I perform a sensitivity analysis on potential cheatgrass distributions using the projections of 10 commonly used atmosphere–ocean general circulation models (AOGCMs) for 2100. The AOGCM projections for precipitation vary considerably, increasing uncertainty in the assessment of invasion risk. Decreased precipitation, particularly in the summer, causes an expansion of suitable land area by up to 45%, elevating invasion risk in parts of Montana, Wyoming, Utah, and Colorado. Conversely, increased precipitation reduces habitat by as much as 70%, decreasing invasion risk. The strong influence of precipitation conditions on this species' distribution suggests that relying on temperature change alone to project future change in plant distributions may be inadequate. A sensitivity analysis provides a framework for identifying key climate variables that may limit invasion, and for assessing invasion risk and restoration opportunities with climate change.     

Movement of sturgeons (Acipenser oxyrinchus oxyrinchus and A. fulvescens) in the St. Lawrence Estuary: A 35-year tagging study

Movement of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and lake sturgeon (A. fulvescens) in the St. Lawrence Estuary (Québec, Canada) are not fully understood. To assess the movement extent of both species, a mark–recapture study was conducted in collaboration with commercial fishermen operating in the St. Lawrence Estuary. Between 1981 and 2015, 3,367 Atlantic sturgeon (fork length 21.8–199.5 cm) and 3,180 lake sturgeon (fork length 17.8–190.8 cm) were tagged and released. Of these, 673 Atlantic sturgeon and 42 lake sturgeon were recaptured. The maximum distances traveled between capture and recapture locations were 1,307 km for Atlantic sturgeon (8 years after initial capture) and 252 km for lake sturgeon (less than 1 year after initial capture). Statistical analyses identified differences in the dispersal distance of both species as revealed by a first component characterized by individuals with short dispersal distances (98% and <35 km for Atlantic sturgeon; 58% and <1 km for lake sturgeon) and a second component characterized by individuals with longer dispersal distances (2% and >600 km for Atlantic sturgeon; 42% and >190 km for lake sturgeon). We suggest that the short dispersal distances detected in the vast majority of Atlantic sturgeon recaptures likely reflect strong site fidelity, highlighting the importance of the St. Lawrence Estuary as a preferred habitat for juveniles and subadults. Although recaptures were low for lake sturgeon because this species is only marginally targeted by commercial fishermen in the St. Lawrence Estuary, our results also showed that this species uses estuarine habitats and that half of the population seems to exhibit strong site fidelity (67% of individuals were recaptured within 2 km).     

The use and misuse of regression models in landscape genetic analyses

The field of landscape genetics has been rapidly evolving, adopting and adapting analytical frameworks to address research questions. Current studies are increasingly using regression‐based frameworks to infer the individual contributions of landscape and habitat variables on genetic differentiation. This paper outlines appropriate and inappropriate uses of multiple regression for these purposes, and demonstrates through simulation the limitations of different analytical frameworks for making correct inference. Of particular concern are recent studies seeking to explain genetic differences by fitting regression models with effective distance variables calculated independently on separate landscape resistance surfaces. When moving across the landscape, organisms cannot respond independently and uniquely to habitat and landscape features. Analyses seeking to understand how landscape features affect gene flow should model a single conductance or resistance surface as a parameterized function of relevant spatial covariates, and estimate the values of these parameters by linking a single set of resistance distances to observed genetic dissimilarity via a loss function. While this loss function may involve a regression‐like step, the associated nuisance parameters are not interpretable in terms of organismal movement and should not be conflated with what is actually of interest: the mapping between spatial covariates and conductance/resistance. The growth and evolution of landscape genetics as a field has been rapid and exciting. It is the goal of this paper to highlight past missteps and demonstrate limitations of current approaches to ensure that future use of regression models will appropriately consider the process being modeled, which will provide clarity to model interpretation.     

The Bio3D packages for structural bioinformatics

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ .     

Improved durable pulmonary vein isolation with shorter procedure times and lower energy levels using RF ablation with ablation index and a stringent lesion contiguity

BackgroundThe single procedure success rates of durable pulmonary vein isolation (PVI) for paroxysmal atrial fibrillation (PAF) varies between 80 and 90%. Ablation index, incorporating contact force, stability, time and power is a more profound parameter of significant lesion size and has been established. Equally important is a stringent contiguity of the lesion set.Methods and resultsA total number of 100 consecutive patients undergoing de-novo catheter ablation for paroxysmal atrial fibrillation (PAF) were analyzed between 2016 and 2019. In the first 50 patients (group A) PVI was performed using a surround flow, contact force catheter (Biosense Webster Thermocool STSF, Biosense Webster, USA) with a drag-and-ablate technique to encircle the PVs. In the following 50 patients (group B), PVI was performed using ablation index and a stringent lesion contiguity with an interlesion distance (ILD) of <5 mm. The baseline characteristics showed no significant differences between both groups. During a mean follow-up of 18 ± 3 months after a single procedure, 36 (72%) patients of group A were free of arrhythmia recurrence versus 43 (86%) patients in group B (p = 0.047). A total of 14 patients (group A: 10 (20%), group B: 4 (8%); underwent a redo-procedure. 7 patients of group A (14%) and 2 patients of group B (4%) showed recovered veins. In 3 patients of group A and 2 patients of group B the PVs were durably isolated. In these patients persistent AF recurrence was caused by extra-PV AF sources. Four patients of group A and three patients of group B had continued paroxysmal or persistent AF but did not undergo redo-procedure. With regard to the procedural data, the procedure time, the total energy and the fluoroscopy time were significantly lower in group B (AI and ILD <5 mm) (128.86 ± 18.19 versus 115.35 ± 15.38; p < 0.05; 1619.16 ± 988.56 versus 1186.26 ± 756.34; p < 0.05; 11.49 ± 3.20 versus 9.66 ± 3.86; p = 0.04). Both procedures were performed with a low number of complications, no pericardial effusion was seen in either group.ConclusionsPVI using ablation index in combination with a stringent lesion contiguity improves clinical outcome after first-time PVI with lower PVI recovery, shorter procedure times, lower total energy and shorter fluoroscopy times and therefore, is more efficient.     

起测径对南盘江流域次生林中枯立木空间结构的影响

树木大小是林分的基础属性,反映个体在森林生态系统过程中扮演的角色和地位。作者于2016-2018年在中国西南地区南盘江流域松栎混交林中建立3块永久性标准固定样地(A、B、C),并用双相关函数g(r)、标记相关函数k_(mm)(r)、标记变差函数γ(r)和k-邻体距离分布函数D~k(r)分析不同大小枯立木的空间结构特征,以揭示林分水平上枯立木的大小和空间结构之间的关系。结果显示:(1)枯立木的起测径(minimum measured diameter, mmd)越小,小尺度上(r=0～5 m)的分布格局趋向聚集状态,但随着起测径的增大(mmd=5～8 cm),随机分布格局几乎占据每个尺度(r=0～20 m)。(2)当起测径等于1～2 cm时,枯立木的大小在小尺度上(r=0～1 m)接近聚集分布,除此之外它一直保持随机分布。(3)当起测径≤4 cm时,枯立木的树种分布集中;反之,它在每个尺度上越接近或成为随机状态。(4)当起测径由1 cm增大至8 cm时,r=0～10 m之内相邻木的株数减少且距离增加,其变化程度受到林分株数的影响。研究表明,枯立木的起测径与其分布格局类型、标记特征以及距离分布紧密相关,暗示同种小树易呈团块死亡,而大径的枯立木偏向随机分布;对比分析枯死木的空间结构需使用统一的起测径标准。     

Effects of Wildlife Forestry on Abundance of Breeding Birds in Bottomland Hardwood Forests of Louisiana

ABSTRACT Effects of silvicultural activities on birds are of increasing interest because of documented national declines in breeding bird populations for some species and the potential that these declines are in part due to changes in forest habitat. Silviculturally induced disturbances have been advocated as a means to achieve suitable forest conditions for priority wildlife species in bottomland hardwood forests. We evaluated how silvicultural activities on conservation lands in bottomland hardwood forests of Louisiana, USA, influenced species-specific densities of breeding birds. Our data were from independent studies, which used standardized point-count surveys for breeding birds in 124 bottomland hardwood forest stands on 12 management areas. We used Program DISTANCE 5.0, Release 2.0 (Thomas et al. 2006) to estimate density for 43 species with >50 detections. For 36 of those species we compared density estimates among harvest regimes (individual selection, group selection, extensive harvest, and no harvest). We observed 10 species with similar densities in those harvest regimes compared with densities in stands not harvested. However, we observed 10 species that were negatively impacted by harvest with greater densities in stands not harvested, 9 species with greater densities in individual selection stands, 4 species with greater densities in group selection stands, and 4 species with greater densities in stands receiving an extensive harvest (e.g., >40% canopy removal). Differences in intensity of harvest influenced densities of breeding birds. Moreover, community-wide avian conservation values of stands subjected to individual and group selection, and stands not harvested, were similar to each other and greater than that of stands subjected to extensive harvest that removed >40% canopy cover. These results have implications for managers estimating breeding bird populations, in addition to predicting changes in bird communities as a result of prescribed and future forest management practices.     

Isoenzyme diversity and cryptic speciation in Juniperus excelsa (Cupressaceae) complex in Iran

An isoenzyme analysis was performed on 109 individuals from 11 populations of Juniperus excelsa complex collected from Iran. A total of 61 allozymes from five enzyme systems were scored. The mean numbers of bands per presumed isoenzyme, ranged from 2.07 to 3.23. The value of Euclidean distance ranged from 1.920 to 4.411. The average value of Shannon diversity index (H′) estimated for each population ranged from 0.317 in the population sampled from ‘Fasa’ to 1.053 in the population of ‘Golestan’, and the average H′ value for each enzyme system ranged from 0.031 (SOD-3) to 1.670 (PPO-1). To reveal the relationships among these populations, a cluster analysis based on Euclidean distances was performed. The results of the analysis suggest recognizing three taxa in the complex in Iran: Juniperus polycarpos subsp. polycarpos, Juniperus polycarpos subsp. turcomanica, and one cryptic species not recorded from Iran until now. Moreover, the analysis presented, does not confirm the occurrence of J. excelsa in Iran.